Awesome. Look forward to trying it out.
-- David Trudgian Ph.D. ________________________________ From: [email protected] [[email protected]] on behalf of David Shteynberg [[email protected]] Sent: Friday, February 07, 2014 2:22 PM To: spctools-discuss Subject: Re: [spctools-discuss] Re: support for Morpheus search algorithm in TPP I was able to make a first stab attempt at it and I was successful after minor modification to the way spectrum_names are encoded in spectrum_query tags in the morpheus pepXML files. After running a simple sed to replace the names with something that wouldn't overlap with anoth file when combined by using the each run's basename I was able to generate results. My PeptideProphet processed analysis for these two searches can be downloaded here: https://www.dropbox.com/s/f5r8j5yj2p2r3b8/morpheus_interact.tgz Here are my sed commands, but I hope this could be fixed within morpheus. sed -i 's/controllerType=0 controllerNumber=1 scan=[0-9]*/OR20080317_S_SILAC-LH_1-1_01/g' OR20080317_S_SILAC-LH_1-1_01.pep.xml sed -i 's/controllerType=0 controllerNumber=1 scan=[0-9]*/OR20080320_S_SILAC-LH_1-1_11/g' OR20080320_S_SILAC-LH_1-1_11.pep.xml Cheers, -David P.S. I expect to merge this into the SVN codebase sooner than later. On Fri, Feb 7, 2014 at 8:35 AM, Dave Trudgian <[email protected]<mailto:[email protected]>> wrote: David, That's the same data. I've made PepXML and the other Morpheus output available at: https://proteomics.swmed.edu/data/morpheus_tpp/ DT On Thursday, February 6, 2014 5:36:35 PM UTC-6, David Shteynberg wrote: I was referring to this data: http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial_v2 However, this is not high res MS/MS either. This would be a good starting point. The decoys and targets don't have to separate by score alone, PeptideProphet should be able to model the plots you show in either case. Cheers, -David On Thu, Feb 6, 2014 at 3:13 PM, Dave Trudgian <[email protected]> wrote: Hi David, Am happy to generate some pepXMLs from the tutorial data, but assuming you mean the stuff at: ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/TPP_Demo2009/ ... I'm not sure that's the best to work with for Morpheus. It's CID Ion-trap MS/MS, which is not Morpheus' target. Morpheus doesn't work as well as other algorithms on low-res MS/MS so I'm not sure if anyone would want to use it like that. I grabbed two of the result sets from the Coon lab site - Yeast analysis with FT HCD or IT CID. The distributions of Morpheus scores are very different. The CID data doesn't even look like target and decoy matches are separable, so I think high-res MS/MS is a must. See attached. DT On Thursday, February 6, 2014 3:44:08 PM UTC-6, David Shteynberg wrote: I was dabbling in this, but running into some issues with morpheus slowing my machine to a point where I was unable to do any other work so I moved to another project. However, I am certainly still interested in this, but I know that pepXML coming out of morpheus may need some work. If you'd be willing to generate some pepXML's from the tutorial data and work with me to correct the pepXML issues I should be able to model the results quite quickly with PeptideProphet. Please let me know if that sounds good to you. Cheers, -David On Thu, Feb 6, 2014 at 12:08 PM, Eric Deutsch <[email protected]> wrote: Hi Dave, at ISB we are not planning this, so please go ahead and let us know how it goes! Regards, Eric From: [email protected] [mailto:[email protected]] On Behalf Of Dave Trudgian Sent: Thursday, February 06, 2014 12:02 PM To: [email protected] Subject: [spctools-discuss] Re: support for Morpheus search algorithm in TPP Craig, just wondering if you or anyone else is working on this? If not I was thinking I would have a go at putting in a Morpheus model for PeptideProphet towards the end of next week. Dave Trudgian On Saturday, November 30, 2013 4:37:30 PM UTC-6, Craig Wenger wrote: Is there a mechanism for adding support for a new search algorithm to the various TPP tools? A few users have requested TPP compatibility for the Morpheus<http://morpheus-ms.sourceforge.net/> search algorithm. It already outputs pepXML. -Craig -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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